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Steady-State Enzyme Kinetics 1
A New 'Microscopic' Look at Steady-state Enzyme Kinetics
Petr Kuzmič BioKin Ltd. http://www.biokin.com SEMINAR: University of Massachusetts Medical School
Worcester, MA
April 6, 2015
1 Outline Part I: Theory steady state enzyme kinetics: a new - - PDF document
A New 'Microscopic' Look at Steady-state Enzyme Kinetics Petr Kuzmi BioKin Ltd. http://www.biokin.com SEMINAR: University of Massachusetts Medical School Worcester, MA April 6, 2015 Steady-State Enzyme Kinetics 1 1 Outline Part I:
Steady-State Enzyme Kinetics 1
Petr Kuzmič BioKin Ltd. http://www.biokin.com SEMINAR: University of Massachusetts Medical School
Worcester, MA
April 6, 2015
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WHAT CAN ENZYME KINETICS DO FOR US?
laboratory measurement
molecular mechanisms
mathematical model
EXAMPLE: Michaelis-Menten (1913)
[substrate] initial rate maximum! rectangular hyperbola v = Vm S/(S+Km) MECHANISM:
substrate and enzyme form a reactive complex, which decomposes into products and regenerates the enzyme catalyst
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time UV/Vis absorbance, A
[Subtrate] rate = dA/dt @ t = 0 slope = “rate”
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Two different mathematical formalisms for initial rate enzyme kinetics:
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MANY ENZYMES THAT ARE TARGETS FOR DRUG DESIGN DISPLAY “FAST CHEMISTRY”
Example: Inosine-5’-monophosphate dehydrogenase from Cryptosporidium parvum chemical step: fast hydride transfer
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The King-Altman method conventionally proceeds in two separate steps: Step One: Derive a rate equation in terms of microscopic rate constants Step Two: Rearrange the original equation in terms of secondary “kinetic constants”
EXPERIMENT:
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micro-constants
“kinetic” constants
Details: Segel, I. (1975) Enzyme Kinetics, Chapter 9, pp. 509-529.
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Step 2 (deriving “Km” etc.) is in principle impossible for branched mechanisms.
Even when Step 2 is possible in principle, it is tedious and error prone.
Measuring “kinetic constants” (Km, Ki, ...) consumes a lot of time and materials.
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TURN THE CONVENTIONAL APPROACH ON ITS HEAD:
CONVENTIONAL APPROACH:
THE NEW APPROACH:
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USE A SUITABLE COMPUTER PROGRAM TO AUTOMATE ALL ALGEBRAIC DERIVATIONS
Kuzmic, P. (2009) Meth. Enzymol. 467, 247-280. INPUT: OUTPUT:
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USE GLOBAL FIT OF MULTI-DIMENSIONAL DATA TO REDUCE THE TOTAL NUMBER OF DATA POINTS
16-20 data points are sufficient
[mechanism] reaction S ---> P modifiers I E + S <==> E.S : ka.S kd.S E.S ---> E + P : kd.P E + I <==> E.I : ka.I kd.I ... [data] variable S ... file d01 | conc I = 0 | label [I] = 0 file d02 | conc I = 1 | label [I] = 1 file d03 | conc I = 2 | label [I] = 2 file d04 | conc I = 4 | label [I] = 4
DYNAFIT INPUT:
global fit
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Data: Dr. Yang Wei (Hedstrom Group, Brandeis University)
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A POTENTIAL TARGET FOR THERAPEUTIC INHIBITOR DESIGN
Overall reaction: inosine-5’-monophosphate + NAD+ → xanthosine-5’-monophosphate + NADH
Chemical mechanism:
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HIGH REACTION RATE MAKES IS NECESSARY TO INVOKE THE STEADY-STATE APPROXIMATION very fast chemistry
IMPDH from Cryptosporidium parvum
irreversible substrate binding
A = B = P = Q = IMP NAD+ XMP NADH UNITS: µM, sec
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THIS SCHEME FOLLOWS FROM STOPPED-FLOW (TRANSIENT) KINETIC EXPERIMENTS
A = B = P = Q = IMP NAD+ XMP NADH UNITS: µM, sec
very fast chemistry irreversible substrate binding
IMPDH from Bacillus anthracis
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1. Validate existing transient kinetic model Are stopped-flow results sufficiently supported by initial rate measurements? 2. Construct the “minimal” initial rate model How far we can go in model complexity based on initial rate data alone? Probing the IMPDH inhibition mechanism from two independent directions.
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substrate “B” and substrate “A”
substrate “B” and product “Q” at constant substrate “A”
substrate “B” and inhibitor “I” at constant substrate “A”
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ADDED A NEW STEP – BINDING OF IMP (substrate “A”) TO THE ENZYME the only fitted rate constants
A = B = P = Q = IMP NAD+ XMP NADH UNITS: µM, sec
[IMP], µM
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THIS CONFIRMS THAT NADH IS REBINDING TO THE E.P COMPLEX (“PRODUCT INHIBITION”)
A = B = P = Q = IMP NAD+ XMP NADH
Kd(NADH) = 90 µM
UNITS: µM, sec
[NADH], µM
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[Inh], µM
0.13
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WHAT IF WE DID NOT HAVE THE STOPPED-FLOW (TRANSIENT) KINETIC RESULTS?
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INITIAL RATE AND STOPPED-FLOW MODELS ARE IN REASONABLY GOOD AGREEMENT
0.27 0.30 Kd ≈ 70 Kd ≈ 90 Kd ≈ 6100 Kd ≈ 5800 Kd ≈ 0.04 Kd ≈ 0.09 15 15
UNITS: µM, sec
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DYNAFIT DOES COMPUTE “Km” AND “Ki” FROM BEST-FIT VALUES OF MICRO-CONSTANTS
microscopic rate constants
derived kinetic constants
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DYNAFIT DOES “KNOW” HOW TO PERFORM KING-ALTMAN ALGEBRAIC DERIVATIONS As displayed in the program’s output: automatically derived kinetic constants:
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“TRUST, BUT VERIFY”
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A Kd is a dissociation equilibrium constant. However, NAD+ does not appear to dissociate.
(NAD)= koff/kon ≈ 0
(NAD) = 450 µM
A Km sometimes is the half-maximum rate substrate concentration (although not in this case).
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turnover number Michaelis constant of NAD+ substrate inhibition constant of NAD+ product inhibition constant of NADH “uncompetitive” Ki for A110
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minimal model (initial rates): Kd = 37 nM King-Altman rate equation automatically derived by DynaFit: Kd
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Kd = 1.3 µM King-Altman rate equation automatically derived by DynaFit: Kd
CONCLUSIONS:
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depending on the exact conditions of the assay.
depends on microscopic details of the catalytic mechanism. Note:
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post-doc, Hedstrom group @ Brandeis All experimental data on IMPDH from Bacillus anthracis
Brandeis University Departments of Biology and Chemistry